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https://gitee.com/sunhf/gprMax.git
已同步 2025-08-08 07:24:19 +08:00
default voxel and optional edge writing
这个提交包含在：
jasminium
@@ -58,7 +58,7 @@ class GeometryView(object):
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def write_xdmf(self, modelrun, numbermodelruns, G):
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filename = self.filename[:-4]
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write_output_file(filename, G)
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write_output_file(filename, G, self.type)
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def write_vtk(self, modelrun, numbermodelruns, G):
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"""Writes the geometry information to a VTK file. Either ImageData (.vti) for a per-cell geometry view, or PolygonalData (.vtp) for a per-cell-edge geometry view.
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274
gprMax/xdmf.py
274
gprMax/xdmf.py
@@ -39,41 +39,6 @@ class Coordinates:
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self.coordinate_count += 1
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def hexCellPicker(grid, i, j, k):
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"""
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This is the ordering of nodes in the hexahedron cell.
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7 --------- 6
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/ /|
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4 --------- 5 2
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| 3 | /
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| / |/
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0 --------- 1
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0 1 2 3 4 5 6 7
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"""
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cell = [
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grid[i][j][k],
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# 1
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grid[i + 1][j][k],
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# 2
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grid[i + 1][j + 1][k],
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# 3
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grid[i][j + 1][k],
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# 4
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grid[i][j][k + 1],
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# 5
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grid[i + 1][j][k + 1],
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# 6
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grid[i + 1][j + 1][k + 1],
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# 7
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grid[i][j + 1][k + 1]
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]
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return cell
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class Solids:
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def __init__(self, fdtd_grid):
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@@ -96,9 +61,44 @@ class SolidLabels():
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self.total_solids = label_grid.n_cells()
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self.solid_labels = np.zeros((self.total_solids, 8), np.float32)
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def hexCellPicker(self, grid, i, j, k):
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"""
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This is the ordering of nodes in the hexahedron cell.
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7 --------- 6
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/ /|
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4 --------- 5 2
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| 3 | /
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| / |/
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0 --------- 1
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0 1 2 3 4 5 6 7
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"""
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cell = [
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grid[i][j][k],
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# 1
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grid[i + 1][j][k],
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# 2
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grid[i + 1][j + 1][k],
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# 3
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grid[i][j + 1][k],
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# 4
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grid[i][j][k + 1],
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# 5
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grid[i + 1][j][k + 1],
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# 6
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grid[i + 1][j + 1][k + 1],
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# 7
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grid[i][j + 1][k + 1]
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]
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return cell
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def add(self, i, j, k):
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solid_labels = hexCellPicker(self.label_grid.grid, i, j, k)
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solid_labels = self.hexCellPicker(self.label_grid.grid, i, j, k)
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self.solid_labels[self.count] = solid_labels
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self.count += 1
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@@ -119,25 +119,23 @@ class Materials:
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self.material_count += 1
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def process_grid(fdtd_grid):
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def process_grid(fdtd_grid, res):
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# Dimensions of the problem domain.
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nx = fdtd_grid.nx
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ny = fdtd_grid.ny
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nz = fdtd_grid.nz
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# useful indices
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i_max = nx - 1
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j_max = ny - 1
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k_max = nz - 1
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# label each node in the space
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labels = np.arange(nx * ny * nz).reshape(nx, ny, nz)
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label_grid = Grid(labels)
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# Edges define the connectivity of the grid.
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edges = Edges(label_grid)
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# Material for each edge
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edge_materials = Materials(fdtd_grid)
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# Define coordinates for each node
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coordinates = Coordinates(fdtd_grid)
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@@ -147,9 +145,12 @@ def process_grid(fdtd_grid):
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# Connectivity for hexhahedron grid
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solid_labels = SolidLabels(label_grid)
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i_max = nx - 1
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j_max = ny - 1
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k_max = nz - 1
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if res == 'f':
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# Edges define the connectivity of the grid.
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edges = Edges(label_grid)
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# Material for each edge
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edge_materials = Materials(fdtd_grid)
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for i, ix in enumerate(labels):
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for j, jx in enumerate(ix):
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@@ -157,80 +158,86 @@ def process_grid(fdtd_grid):
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label = labels[i][j][k]
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# Each vertex can have varying numbers of edges
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# Type 1 vertex
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if i < i_max and j < j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 2)
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# Only this node can support a cell
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solids.add_solid(i, j, k)
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solid_labels.add(i, j, k)
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# Type 2 vertex
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elif i < i_max and j == j_max and k == k_max:
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 0)
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if res == 'f':
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# Each vertex can have varying numbers of edges
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# Type 1 vertex
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if i < i_max and j < j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i, j, k + 1)
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# Type 7 vertex
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elif i < i_max and j == j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 2)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 2)
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# Type 6 vertex
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elif i == i_max and j == j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 2)
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# Only this node can support a cell
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# Type 5 vertex
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elif i == i_max and j < j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 2)
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edge_materials.add_material(i, j, k, 1)
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# Type 2 vertex
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elif i < i_max and j == j_max and k == k_max:
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 0)
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# Type 4 vertex
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elif i == i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 1)
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# Type 7 vertex
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elif i < i_max and j == j_max and k < k_max:
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edges.add_edge(label, i + 1, j, k)
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 0)
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edge_materials.add_material(i, j, k, 2)
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# Type 8 vertex
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elif i < i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 0)
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# Type 6 vertex
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elif i == i_max and j == j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edge_materials.add_material(i, j, k, 2)
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# Type 3 vertex
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# Has no new connectivity
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elif i == i_max and j == j_max and k == k_max:
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pass
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else:
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print('oh no')
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# Type 5 vertex
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elif i == i_max and j < j_max and k < k_max:
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edges.add_edge(label, i, j, k + 1)
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 2)
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edge_materials.add_material(i, j, k, 1)
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# Type 4 vertex
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elif i == i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edge_materials.add_material(i, j, k, 1)
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# Type 8 vertex
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elif i < i_max and j < j_max and k == k_max:
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edges.add_edge(label, i, j + 1, k)
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edges.add_edge(label, i + 1, j, k)
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edge_materials.add_material(i, j, k, 1)
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edge_materials.add_material(i, j, k, 0)
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# Type 3 vertex
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# Has no new connectivity
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elif i == i_max and j == j_max and k == k_max:
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pass
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else:
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print('oh no')
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# Add the coordinates
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coordinates.add_coordinate(i, j, k)
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return {
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data = {
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'coordinates': coordinates,
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'solids': solids,
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'solid_labels': solid_labels,
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'edges': edges,
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'edge_materials': edge_materials,
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}
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if res == 'f':
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data['edges'] = edges
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data['edge_materials'] = edge_materials
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def write_output_file(filename, grid):
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return data
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data = process_grid(grid)
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def write_output_file(filename, grid, res):
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data = process_grid(grid, res)
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data['filename'] = filename
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data['xml_doc'] = create_xdmf_markup(data)
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@@ -246,14 +253,17 @@ def write_xml_doc(options):
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def write_H5file(options):
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f = h5py.File(options['filename'] + '.h5', "w")
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coords = f.create_group("mesh")
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coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
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coords.create_dataset('connectivity', data=options['edges'].edges)
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coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
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data = f.create_group("data")
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f = h5py.File(options['filename'] + '.h5', "w")
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coords = f.create_group("mesh")
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data = f.create_group("data")
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coords.create_dataset('coordinates', data=options['coordinates'].coordinates)
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coords.create_dataset('solid_connectivity', data=options['solid_labels'].solid_labels)
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data.create_dataset('solids', data=options['solids'].solids)
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if 'edges' in options:
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data.create_dataset('materials', data=options['edge_materials'].materials)
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data.create_dataset('solids', data=options['solids'].solids)
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coords.create_dataset('connectivity', data=options['edges'].edges)
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def create_xdmf_markup(options):
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@@ -264,36 +274,40 @@ def create_xdmf_markup(options):
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domain_el = etree.Element("Domain")
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xdmf_el.append(domain_el)
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grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
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domain_el.append(grid_el)
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# Create the grid node
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topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
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grid_el.append(topology_el)
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topology_dimensions = "{} 2".format(options['edges'].total_edges)
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top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
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top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
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topology_el.append(top_data_el)
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# Create the Geometry node
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geometry_el = etree.Element("Geometry", GeometryType="XYZ")
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grid_el.append(geometry_el)
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# Create the origin coordinates
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coordinates_dimensions = "{} 3".format(options['coordinates'].total_coordinates)
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origin_el = etree.Element("DataItem", Dimensions=coordinates_dimensions, NumberType="Float", Precision="8", Format="HDF")
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origin_el.text = "{}:/mesh/coordinates".format(options['filename'] + '.h5')
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geometry_el.append(origin_el)
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# Create the materials attribute
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attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
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grid_el.append(attr_el)
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# Check if there are edges to write
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if 'edges' in options:
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materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
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materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
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materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
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attr_el.append(materials_el)
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grid_el = etree.Element("Grid", Name="Edges", GridType="Uniform")
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domain_el.append(grid_el)
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# Create the grid node
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topology_el = etree.Element("Topology", TopologyType="Polyline", NumberOfElements=str(options['edges'].total_edges))
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grid_el.append(topology_el)
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topology_dimensions = "{} 2".format(options['edges'].total_edges)
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top_data_el = etree.Element("DataItem", Dimensions=topology_dimensions, NumberType="Float", Precision="8", Format="HDF")
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top_data_el.text = "{}:/mesh/connectivity".format(options['filename'] + '.h5')
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topology_el.append(top_data_el)
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# Create the Geometry node
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grid_el.append(copy.deepcopy(geometry_el))
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# Create the origin coordinates
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# Create the materials attribute
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attr_el = etree.Element("Attribute", Center="Cell", Name="Edge_Materials")
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grid_el.append(attr_el)
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materials_dimensions = "{} 1".format(options['edge_materials'].material_count)
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materials_el = etree.Element("DataItem", Dimensions=materials_dimensions, NumberType="Float", Precision="8", Format="HDF")
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materials_el.text = "{}:/data/materials".format(options['filename'] + '.h5')
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attr_el.append(materials_el)
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v_grid_el = etree.Element("Grid", Name="Voxel", GridType="Uniform")
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domain_el.append(v_grid_el)
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